World Families Forums - New SNP Downstream of L21

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In the P312 Project of those 531=12, I would bet that they have not tested for L21 and if they did they would all go L21+. Can you check if they have or not?4131 Thomas Rice, Gloucester 59275 John Burnett, b.1794 Fettercairn, Kincardineshire73014 Albert C. Jacobson, b. abt 1862, Norway

In the P312 Project of those 531=12, I would bet that they have not tested for L21 and if they did they would all go L21+. Can you check if they have or not?4131 Thomas Rice, Gloucester 59275 John Burnett, b.1794 Fettercairn, Kincardineshire73014 Albert C. Jacobson, b. abt 1862, Norway

You skipped Ranney, kit 93184.

Look at the categories those guys are in. They are all in R-P312* categories. I don't put people in R-P312* categories unless they are P312+ and negative for everything downstream of it.

That is why I wrote that I pulled them all from L21- categories. Just to be on the safe side I rechecked all of them just now, and they are all L21-.

The only men still untested for L21 in the R-P312 and Subclades Project are either in the "R-P312 (Need L21 Test results)" category or in "Unassigned Members".

I believe it is, but there are other parts of it that are more important, I think, like having 19-24 at YCA II.

Along with 10 at 391 and 30 at 389ii, all of which I have, after that the similarities disappear, very odd but time will tell.

As it happens I’ve noticed a 7 off match on 67 somewhere in Wales, the only one I have that is close enough for FTDNA to report, the next nearest is 12 I believe. Unfortunately he only appears in my ancestor origins page, and I can’t find him in Ysearch either, ho hum.

Are any of Robert Hughe's 17-14-10 / Wales modal 1 cluster in the WTY or doing an L159 test? I just noticed a pattern holds across both this cluster and the Leinster cluster. It may be nothing, but this loose pattern holds across these two groups and not to many other L21* guys. They are on both sides of the Irish Sea. Of course, maybe I'm seeing things.

I wasn't looking for a L159+ look-alike cluster to the Leinster guys, when I stumbled on this. I have identified/listed about 40 "potential" clusters of R-L21*. A number of these are variants of traditional modals - i.e. Scots, Wales 1, Wales 2, Wales 3, Irish TII, Irish TIII, Unknown Scots, Cluster X, Irish Sea/Leinster, etc.I started looking for relationships among the clusters where there were "clean breaks," not a bunch of random clutter. I noticed that DYS448<=18 and DYS449<=30 showed both Leinster/Irish Sea and the Wales 1 17-14-10 guys.None of the other clusters that I've seen have this so it is a pretty clean break. The only exception is a few Wales 2 Cadwgon guys have it also.

To make things clear, there was no NEW SNP found in your DNA. However there were two things observed that distinguish you from all other R-L21 participants:

First you have a 14.3 micro-allele at DYS464 which is essentially a 1 bp deletion SNP in one of the 4 DYS464 amplicons. We didn't sequence this part of your DNA (we only measured the length of the segments) so we can't tell if the SNP is inside the repeat unit or in the flanking region. If the deletion is in the flanking region it is as good as a new SNP and could be used as a marker for a new R-L21 branch. If it is inside the repeat then chances are high that it is rather unstable. It may be a good idea to do further research on your DNA and try to sequence at least the flanking regions of your DYS464 alleles. Also note that you have a DYS464X cccc configuration (No G-type allele!). This is definitely a signature that lets you exclude all R-L21 with a G-type allele from being a descendant of the first person in your male lineage that had the cccc haplotype.

The second irregular feature is the L69+ marker which hasn't been observed in other R-L21 persons so far. The L69/L159 polymorphism is essentially a SNP/STR oxymoron. The base change happens right at the intersection of a poly G homopolymer and a GT dinucleotide repeat.

In the case of L69+ the poly G is shortened from 6 to 4 bases and the dinucleotid repeat gains one unit.In the case of L159+ the poly G is elongated from 6 to 8 bases and the dinucleotid repeat looses one unit.

This alignment of sequences may make this clearer:

AAACTGGGGGGGGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGCG (L69+)AAACTGGGGGGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGCG (HUGO and most others)AAACTGGGGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGCG (L159+)L69......^L159.......^(note that the GT repeat count may vary and is disregarded for the L96/L159 status)

The L69/L159 polymorphism is certainly not a UEP because it has been observed in various other haplogroups and we are certainly at the very beginning of understanding its mechanism and phylogenetic relevance. We have to be careful because it can "mutate" back like a regular STR. However with caution it may be a good help to sort out genealogies and haplotype clusters. Only further testing will answer the question how useful this polymorphism may be and what mutation frequency we can expect.

To make things clear, there was no NEW SNP found in your DNA. However there were two things observed that distinguish you from all other R-L21 participants:

First you have a 14.3 micro-allele at DYS464 which is essentially a 1 bp deletion SNP in one of the 4 DYS464 amplicons. We didn't sequence this part of your DNA (we only measured the length of the segments) so we can't tell if the SNP is inside the repeat unit or in the flanking region. If the deletion is in the flanking region it is as good as a new SNP and could be used as a marker for a new R-L21 branch. If it is inside the repeat then chances are high that it is rather unstable. It may be a good idea to do further research on your DNA and try to sequence at least the flanking regions of your DYS464 alleles. Also note that you have a DYS464X cccc configuration (No G-type allele!). This is definitely a signature that lets you exclude all R-L21 with a G-type allele from being a descendant of the first person in your male lineage that had the cccc haplotype.

The second irregular feature is the L69+ marker which hasn't been observed in other R-L21 persons so far. The L69/L159 polymorphism is essentially a SNP/STR oxymoron. The base change happens right at the intersection of a poly G homopolymer and a GT dinucleotide repeat.

In the case of L69+ the poly G is shortened from 6 to 4 bases and the dinucleotid repeat gains one unit.In the case of L159+ the poly G is elongated from 6 to 8 bases and the dinucleotid repeat looses one unit.

This alignment of sequences may make this clearer:

AAACTGGGGGGGGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGCG (L69+)AAACTGGGGGGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGCG (HUGO and most others)AAACTGGGGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGCG (L159+)L69......^L159.......^(note that the GT repeat count may vary and is disregarded for the L96/L159 status)

The L69/L159 polymorphism is certainly not a UEP because it has been observed in various other haplogroups and we are certainly at the very beginning of understanding its mechanism and phylogenetic relevance. We have to be careful because it can "mutate" back like a regular STR. However with caution it may be a good help to sort out genealogies and haplotype clusters. Only further testing will answer the question how useful this polymorphism may be and what mutation frequency we can expect.

Bernard[/size]

Some of that I don't really understand, but the stuff about 464 certainly sounds interesting and promising.

I guess we should all have our 464 tested for the c/g pattern. I have never done that yet.

Yeah, the 464X test has been really fruitful for the Leinster cluster. It would be really interesting to have more L21 test for it.

I wish the FTDNA reporting mechanism could list the 464x results. It's pretty inexpensive, but I think it is more important to get to 67 markers and do a deep clade test (or deep claded extended) if you haven't already.

I'm 15c-15c-17c-17g or 3c1g. I guess 3c1g is very common. The 2c2g found by many if not most of the Leinster cluster is uncommon. My understanding is that 464x mutations to 2c2g or to 4c or anything other than 3c1g is not as definitive (stable) as an SNP but more definitive (slower moving) than an STR.

I don't understand the statement that the "14.3 micro-allele at DYS464 which is essentially a 1 bp deletion SNP in one of the 4 DYS464 amplicons." I don't see any comments like that related to a 464x test result. Should there be or is the WTY testing the only way to know about this deletion?

At least your in company, mine is ccgc. I have asked FtDNA what the mutations are that get to that point. I can not find any discussion on that much detail. gggg>cccg> then I do not know what the next mutations to take me to my ccgc.

Yes. Thanks. The document does not explain if the mutation occurs in any sequence and in what order, if any. Since there is no additional detail, one could assume it is random in any 464 marker so I guess the question is: Does the single 'g' that most R1b's have, randomly appear at any position?

All Krahn states: "Most R1b males that we have tested show 3 C-types and 1 G-type. All other haplogroups (including R1a) show 4 G-types."